RetrogeneDB ID: retro_cjac_2498

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:2844287..2844938(+)
• Located in intron of: ENSCJAG00000018204

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSCJAG00000003123
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_cjac_2498
ATGCCCATGACACTGGGGTACTGGGACCTCCGCGGGTTGGCCCACGCCATCCGCCTGCTCCTGGAATACACAGACTCAAG
CTACGAGGAAAAGACCTACACGATGGGGGACGCTCCTGACTATGACAGAAGCCAGTGGCTGAAGGAAAAATTCAAGCTGG
GCCTGGACTTTCCCAATCTGCCCTATTTGATTGATGGGGCTCACAAGATCACCCAGAGCAACGCCATCCTGCGCTACATT
GCCCGCAAACACAACCTGTGTGGGGAGACAGAAGAGGAGAAGATCGTGTGGACATTTTGGAGAACCAGACCATGGACACT
CGGATGCAGCTGGCCATGCTCTGCTACAACCCAGAATTTGAGAAACTGAAGCCAAAGTACTTGGAGGAACTCCCTGAAAA
GTTAAAGTTCTACTCCCCAGTTTCTGGGGAAGCGACCATGGTTTGCAGGAGACAAGATAACCTTTGTGGATTTCCTCGCC
TATGACATTCTTGACCACAACCGTATATTTGAGCCCAGTTGCCTGGACGCTTTCCCAAACCTGAAGGACTTTATGTCCCG
ATTCGAGGGTTTGAAGATCTCTGCCTACATGAAGTCCAGCAGATTCGTCCCAGGTCTTTTGTTTGGAAAGTCAGCTACAT
GGAACAGCAAA

Alignment

ORF - retro_cjac_2498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLKEKFKLGLDFPNLPYLIDGAHKI
          MPMTLGYWD.RGLAHAIRLLLEYTDSSYEEK.YTMGDAPDYDRSQWLKEKFKLGLDFPNLPYLIDGAHKI
Retrocopy MPMTLGYWDLRGLAHAIRLLLEYTDSSYEEKTYTMGDAPDYDRSQWLKEKFKLGLDFPNLPYLIDGAHKI

Parental  TQSNAILRYIARKHSLCGETEEEKI-RVDILENQTMDTRMQLAMLCYNPEFEKLKPKYLEELPEKLKLYS
          TQSNAILRYIARKH.LCGETEEEKI.RVDILENQTMDTRMQLAMLCYNPEFEKLKPKYLEELPEKLK.YS
Retrocopy TQSNAILRYIARKHNLCGETEEEKI<RVDILENQTMDTRMQLAMLCYNPEFEKLKPKYLEELPEKLKFYS

Parental  -QFLGKRPWFAGDKITFVDFLAYDVLDQNRIFEPSCLDAFPNLKDFMSRFEGLKKISAYMKSSRFVPGLL
          .QFLGKRPWFAGDKITFVDFLAYD.LD.NRIFEPSCLDAFPNLKDFMSRFEGL.KISAYMKSSRFVPGLL
Retrocopy >QFLGKRPWFAGDKITFVDFLAYDILDHNRIFEPSCLDAFPNLKDFMSRFEGL-KISAYMKSSRFVPGLL

Parental  FGKSATWNSK
          FGKSATWNSK
Retrocopy FGKSATWNSK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.98 RPM	24.03 RPM
SRP051959_heart	0.77 RPM	18.65 RPM
SRP051959_kidney	0.51 RPM	30.02 RPM
SRP051959_liver	0.69 RPM	15.47 RPM
SRP051959_lung	1.30 RPM	19.57 RPM
SRP051959_lymph_node	1.42 RPM	13.36 RPM
SRP051959_skeletal_muscle	0.79 RPM	8.84 RPM
SRP051959_spleen	0.95 RPM	22.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2498 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498 , retro_cjac_3004, retro_cjac_3084, retro_cjac_811,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Gorilla gorilla	ENSGGOG00000005148	2 retrocopies	retro_ggor_1913, retro_ggor_2459,
Nomascus leucogenys	ENSNLEG00000003194	2 retrocopies	retro_nleu_1546, retro_nleu_504,
Pongo abelii	ENSPPYG00000001064	2 retrocopies	retro_pabe_2218, retro_pabe_2990,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859, retro_ptro_2468,